0001 function varargout=marsbar(varargin)
0002
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0014
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0037 MBver = '0.45';
0038
0039
0040 global MARS;
0041
0042
0043
0044 if nargin == 0, Action='Startup'; else, Action = varargin{1}; end
0045
0046
0047 switch lower(Action), case 'startup'
0048
0049
0050
0051 warning backtrace
0052
0053
0054 splashf = ~marsbar('is_started');
0055
0056
0057 marsbar('on');
0058
0059
0060
0061
0062 mlv = version; mlv = str2num(mlv(1:3));
0063 if mlv >= 7 && strcmp(computer, 'GLNX86')
0064 if usejava('jvm')
0065 setappdata(0,'UseNativeSystemDialogs',false)
0066 else
0067 warning(['Matlab 7, linux, no java, please see FAQ for '...
0068 'information on problems with file selection dialogs']);
0069 end
0070 end
0071
0072
0073
0074 S = get(0,'ScreenSize');
0075 if all(S==1), error('Can''t open any graphics windows...'), end
0076 PF = spm_platform('fonts');
0077
0078
0079
0080 if splashf
0081 marsbar('splash');
0082 end
0083
0084
0085
0086 Fmenu = marsbar('CreateMenuWin','off');
0087
0088
0089
0090 set([Fmenu],'Visible','on')
0091
0092
0093 case 'on'
0094
0095
0096
0097
0098 mbpath = fileparts(which('marsbar.m'));
0099 spmV = mars_utils('spm_version');
0100 m_spm_paths = {'spm99', 'spm2', 'spm5'};
0101 v_path = lower(spmV);
0102
0103 switch v_path
0104 case {'spm8', 'spm12b', 'spm12'}
0105 v_path = 'spm5';
0106 end
0107 w_s = warning;
0108 warning off
0109 for p = m_spm_paths(~ismember(m_spm_paths, v_path))
0110 rmpath(fullfile(mbpath, char(p)))
0111 end
0112 warning(w_s)
0113 MARS.ADDPATHS = {fullfile(mbpath, v_path)};
0114 addpath(MARS.ADDPATHS{:}, '-begin');
0115 fprintf('MarsBaR analysis functions prepended to path\n');
0116
0117
0118 mars_veropts('defaults');
0119
0120
0121
0122 if isfield(MARS, 'ARMOIRE')
0123 o = MARS.ARMOIRE;
0124 else
0125 o = marmoire;
0126 end
0127
0128 spm_design_filter = mars_veropts('design_filter_spec');
0129 filter_specs = {[spm_design_filter(1,:);...
0130 {'*_mdes.mat','MarsBaR: *_mdes.mat'}; ...
0131 spm_design_filter(2:end,:)], ...
0132 {'*_mdata.mat','MarsBaR data file (*_mdata.mat)'},...
0133 {'*_mres.mat', 'MarsBaR results (*_mres.mat)'}};
0134
0135 o = add_if_absent(o, 'def_design', ...
0136 struct('default_file_name', 'untitled_mdes.mat',...
0137 'filter_spec', {filter_specs{1}},...
0138 'title', 'Default design',...
0139 'set_action','mars_arm_call(''set_design'',o,item,old_o)'));
0140 o = add_if_absent(o, 'roi_data',...
0141 struct('default_file_name', 'untitled_mdata.mat',...
0142 'filter_spec', {filter_specs{2}},...
0143 'title', 'ROI data',...
0144 'set_action','mars_arm_call(''set_data'',o,item,old_o)'));
0145 o = add_if_absent(o, 'est_design',...
0146 struct('default_file_name', 'untitled_mres.mat',...
0147 'filter_spec', {filter_specs{3}},...
0148 'title', 'MarsBaR estimated design',...
0149 'set_action', 'mars_arm_call(''set_results'',o,item,old_o)'));
0150 MARS.ARMOIRE = o;
0151
0152
0153 if ~isfield(MARS, 'WORKSPACE'), MARS.WORKSPACE = []; end
0154
0155
0156 if ~mars_struct('isthere', MARS, 'OPTIONS')
0157 loadf = 1;
0158 MARS.OPTIONS = [];
0159 else
0160 loadf = 0;
0161 end
0162 [mbdefs sourcestr] = mars_options('Defaults');
0163 MARS.OPTIONS = mars_options('fill',MARS.OPTIONS, mbdefs);
0164 mars_options('put');
0165 if loadf
0166 fprintf('Loaded MarsBaR defaults from %s\n',sourcestr);
0167 end
0168
0169
0170
0171
0172 maroi;
0173
0174
0175 case 'off'
0176
0177
0178
0179 varargout = {0};
0180
0181
0182 if ~marsbar('is_started'), return, end
0183
0184
0185 btn = mars_arm('save_ui', 'all', struct('ync', 1, 'no_no_save', 1));
0186 if btn == -1, varargout = {-1}; return, end
0187
0188
0189 rmpath(MARS.ADDPATHS{:});
0190 fprintf('MarsBaR analysis functions removed from path\n');
0191
0192
0193 case 'quit'
0194
0195
0196
0197
0198
0199 if marsbar('off') == -1, return, end
0200
0201
0202 if ~marsbar('is_started'), return, end
0203
0204
0205 delete(spm_figure('FindWin','MarsBaR'))
0206 fprintf('Au revoir...\n\n')
0207
0208
0209 case 'is_started'
0210
0211
0212 varargout = {~isempty(MARS)};
0213
0214
0215 case 'cfgfile'
0216
0217
0218 cfgfile = 'marsbarcfg.mat';
0219 varargout = {which(cfgfile), cfgfile};
0220
0221
0222 case 'createmenuwin'
0223
0224
0225 if nargin<2, Vis='on'; else, Vis=varargin{2}; end
0226
0227
0228 delete(spm_figure('FindWin','MarsBaR'))
0229
0230
0231 [MBver,MBc] = marsbar('Ver');
0232
0233
0234
0235 WS = spm('WinScale');
0236 FS = spm('FontSizes');
0237 PF = spm_platform('fonts');
0238 Rect = [50 600 300 275];
0239 bno = 6; bgno = bno+1;
0240 bgapr = 0.25;
0241 bh = Rect(4) / (bno + bgno*bgapr);
0242 gh = bh * bgapr;
0243 by = fliplr(cumsum([0 ones(1, bno-1)*(bh+gh)])+gh);
0244 bx = Rect(3)*0.1;
0245 bw = Rect(3)*0.8;
0246 Fmenu = figure('IntegerHandle','off',...
0247 'Name',sprintf('%s',MBc),...
0248 'NumberTitle','off',...
0249 'Tag','MarsBaR',...
0250 'Position',Rect.*WS,...
0251 'Resize','off',...
0252 'Color',[1 1 1]*.8,...
0253 'UserData',struct('MBver',MBver,'MBc',MBc),...
0254 'MenuBar','none',...
0255 'DefaultTextFontName',PF.helvetica,...
0256 'DefaultTextFontSize',FS(12),...
0257 'DefaultUicontrolFontName',PF.helvetica,...
0258 'DefaultUicontrolFontSize',FS(12),...
0259 'DefaultUicontrolInterruptible','on',...
0260 'Renderer','painters',...
0261 'Visible','off');
0262
0263
0264
0265
0266 funcs = {'mars_display_roi(''display'');',...
0267 'mars_blob_ui;',...
0268 'marsbar(''buildroi'');',...
0269 'marsbar(''transform'');',...
0270 'marsbar(''import_rois'');',...
0271 'marsbar(''export_rois'');'};
0272
0273 uicontrol(Fmenu,'Style','PopUp',...
0274 'String',['ROI definition',...
0275 '|View...'...
0276 '|Get SPM cluster(s)...'...
0277 '|Build...',...
0278 '|Transform...',...
0279 '|Import...',...
0280 '|Export...'],...
0281 'Position',[bx by(1) bw bh].*WS,...
0282 'ToolTipString','Draw / build / combine ROIs...',...
0283 'CallBack','spm(''PopUpCB'',gcbo)',...
0284 'UserData',funcs);
0285
0286
0287 fw_st = 'struct(''force'', 1, ''warn_empty'', 1)';
0288 funcs = {...
0289 'marsbar(''make_design'', ''pet'');',...
0290 'marsbar(''make_design'', ''fmri'');',...
0291 'marsbar(''make_design'', ''basic'');',...
0292 'marsbar(''design_report'')',...
0293 'marsbar(''design_filter'')',...
0294 'marsbar(''add_images'')',...
0295 'marsbar(''edit_filter'')',...
0296 'marsbar(''check_images'')',...
0297 'marsbar(''list_images'')',...
0298 'marsbar(''ana_cd'')',...
0299 'marsbar(''ana_desmooth'')',...
0300 'marsbar(''def_from_est'')',...
0301 'marsbar(''set_def'')',...
0302 ['mars_arm(''save_ui'', ''def_design'', ' fw_st ');'],...
0303 'mars_arm(''show_summary'', ''def_design'')'};
0304
0305 uicontrol(Fmenu,'Style','PopUp',...
0306 'String',['Design...'...
0307 '|PET models',...
0308 '|FMRI models',...
0309 '|Basic models',...
0310 '|Explore',...
0311 '|Frequencies (event+data)',...
0312 '|Add images to FMRI design',...
0313 '|Add/edit filter for FMRI design',...
0314 '|Check image names in design',...
0315 '|List image names to console',...
0316 '|Change design path to images',...
0317 '|Convert to unsmoothed',...
0318 '|Set design from estimated',...
0319 '|Set design from file',...
0320 '|Save design to file',...
0321 '|Show default design summary'],...
0322 'Position',[bx by(2) bw bh].*WS,...
0323 'ToolTipString','Set/specify design...',...
0324 'CallBack','spm(''PopUpCB'',gcbo)',...
0325 'UserData',funcs);
0326
0327
0328 funcs = {'marsbar(''extract_data'', ''default'');',...
0329 'marsbar(''extract_data'', ''full'');',...
0330 'marsbar(''set_defregion'');',...
0331 'marsbar(''plot_data'', ''raw'');',...
0332 'marsbar(''plot_data'', ''full'');',...
0333 'marsbar(''import_data'');',...
0334 'marsbar(''export_data'');',...
0335 'marsbar(''split_data'');',...
0336 'marsbar(''join_data'');',...
0337 'mars_arm(''set_ui'', ''roi_data'');',...
0338 ['mars_arm(''save_ui'', ''roi_data'', ' fw_st ');'],...
0339 'mars_arm(''show_summary'', ''roi_data'')'};
0340
0341 uicontrol(Fmenu,'Style','PopUp',...
0342 'String',['Data...'...
0343 '|Extract ROI data (default)',...
0344 '|Extract ROI data (full options)',...
0345 '|Default region...',...
0346 '|Plot data (simple)',...
0347 '|Plot data (full)',...
0348 '|Import data',...
0349 '|Export data',...
0350 '|Split regions into files',...
0351 '|Merge data files',...
0352 '|Set data from file',...
0353 '|Save data to file',...
0354 '|Show data summary'],...
0355 'Position',[bx by(3) bw bh].*WS,...
0356 'ToolTipString','Extract/set/save data...',...
0357 'CallBack','spm(''PopUpCB'',gcbo)',...
0358 'UserData',funcs);
0359
0360
0361 funcs = {...
0362 'marsbar(''estimate'');',...
0363 'marsbar(''merge_contrasts'');',...
0364 'marsbar(''refresh_contrasts'');',...
0365 'marsbar(''add_trial_f'');',...
0366 'marsbar(''set_defcon'');',...
0367 'marsbar(''set_defregion'');',...
0368 'marsbar(''plot_residuals'');',...
0369 'marsbar(''spm_graph'');',...
0370 'marsbar(''stat_table'');',...
0371 'marsbar(''signal_change'');',...
0372 'marsbar(''fitted_events'');',...
0373 'marsbar(''fir_events'');',...
0374 'marsbar(''add_events_by_name'');',...
0375 'marsbar(''set_results'');',...
0376 ['mars_arm(''save_ui'', ''est_design'', ' fw_st ');'],...
0377 'mars_arm(''show_summary'', ''est_design'')'};
0378
0379 uicontrol(Fmenu,'Style','PopUp',...
0380 'String',['Results...'...
0381 '|Estimate results',...
0382 '|Import contrasts',...
0383 '|Refresh F contrasts',...
0384 '|Add trial-specific F',...
0385 '|Default contrast...',...
0386 '|Default region...',...
0387 '|Plot residuals',...
0388 '|MarsBaR SPM graph',...
0389 '|Statistic table',...
0390 '|% signal change',...
0391 '|Fitted event time course',...
0392 '|FIR event time course',...
0393 '|Add event types by name',...
0394 '|Set results from file',...
0395 '|Save results to file',...
0396 '|Show estimated design summary'],...
0397 'Position',[bx by(4) bw bh].*WS,...
0398 'ToolTipString','Write/display contrasts...',...
0399 'CallBack','spm(''PopUpCB'',gcbo)',...
0400 'UserData',funcs);
0401
0402
0403 funcs = {['global MARS; '...
0404 'MARS.OPTIONS=mars_options(''edit'');mars_options(''put'');'],...
0405 ['global MARS; '...
0406 '[MARS.OPTIONS str]=mars_options(''defaults'');' ...
0407 'mars_options(''put''); '...
0408 'fprintf(''Defaults loaded from %s\n'', str)'],...
0409 ['global MARS; '...
0410 '[MARS.OPTIONS str]=mars_options(''basedefaults'');' ...
0411 'mars_options(''put''); '...
0412 'fprintf(''Defaults loaded from %s\n'', str)'],...
0413 ['global MARS; '...
0414 'MARS.OPTIONS=mars_options(''load'');mars_options(''put'');'],...
0415 'mars_options(''save'');'...
0416 };
0417
0418 uicontrol(Fmenu,'Style','PopUp',...
0419 'String',['Options...'...
0420 '|Edit options'...
0421 '|Restore defaults'...
0422 '|Base defaults',...
0423 '|Set options from file'...
0424 '|Save options to file'],...
0425 'Position',[bx by(5) bw bh].*WS,...
0426 'ToolTipString','Load/save/edit MarsBaR options',...
0427 'CallBack','spm(''PopUpCB'',gcbo)',...
0428 'UserData',funcs);
0429
0430
0431 uicontrol(Fmenu,'String','Quit',...
0432 'Position',[bx by(6) bw bh].*WS,...
0433 'ToolTipString','exit MarsBaR',...
0434 'ForeGroundColor','r',...
0435 'Interruptible','off',...
0436 'CallBack','marsbar(''Quit'')');
0437
0438
0439
0440 set(Fmenu,'CloseRequestFcn','marsbar(''Quit'')')
0441 set(Fmenu,'Visible',Vis)
0442
0443 varargout = {Fmenu};
0444
0445
0446 case {'ver', 'version'}
0447
0448
0449
0450 varargout = {MBver, 'MarsBaR - Marseille ROI toolbox'};
0451
0452
0453 case 'splash'
0454
0455
0456
0457
0458 WS = spm('WinScale');
0459 [X,map] = imread('marsbar.jpg');
0460 aspct = size(X,1) / size(X,2);
0461 ww = 400;
0462 srect = [200 300 ww ww*aspct] .* WS;
0463 h = figure('visible','off',...
0464 'menubar','none',...
0465 'numbertitle','off',...
0466 'name','Welcome to MarsBaR',...
0467 'pos',srect);
0468 im = image(X);
0469 colormap(map);
0470 ax = get(im, 'Parent');
0471 axis off;
0472 axis image;
0473 axis tight;
0474 set(ax,'plotboxaspectratiomode','manual',...
0475 'unit','pixels',...
0476 'pos',[0 0 srect(3:4)]);
0477 set(h,'visible','on');
0478 pause(3);
0479 close(h);
0480
0481
0482 case 'buildroi'
0483
0484
0485
0486
0487 varargout = {[]};
0488 o = mars_build_roi;
0489 if ~isempty(o)
0490 varargout = {marsbar('saveroi', o)};
0491 end
0492
0493
0494 case 'transform'
0495
0496
0497
0498 marsbar('mars_menu', 'Transform ROI', 'Transform:', ...
0499 {{'combinerois'},{'flip_lr'}},...
0500 {'Combine ROIs','Flip L/R'});
0501
0502
0503 case 'import_rois'
0504
0505
0506
0507
0508 marsbar('mars_menu', 'Import ROIs', 'Import ROIs from:',...
0509 {{'img2rois','c'},...
0510 {'img2rois','i'}},...
0511 {'cluster image',...
0512 'number labelled ROI image'});
0513
0514
0515 case 'export_rois'
0516
0517
0518
0519
0520 marsbar('mars_menu', 'Export ROI(s)', 'Export ROI(s) to:',...
0521 {{'roi_as_image'},...
0522 {'rois2img', 'c'},...
0523 {'rois2img', 'i'}},...
0524 {'image', 'cluster image',...
0525 'number labelled ROI image'});
0526
0527
0528 case 'img2rois'
0529
0530
0531
0532
0533 if nargin < 2
0534 roi_type = 'c';
0535 else
0536 roi_type = varargin{2};
0537 end
0538 mars_img2rois('','','',roi_type);
0539
0540
0541 case 'rois2img'
0542
0543
0544
0545
0546 if nargin < 2
0547 roi_type = 'c';
0548 else
0549 roi_type = varargin{2};
0550 end
0551 mars_rois2img('','','',roi_type);
0552
0553
0554 case 'saveroi'
0555
0556
0557
0558
0559
0560
0561
0562 if nargin < 2 || isempty(varargin{2})
0563 return
0564 end
0565 if nargin < 3
0566 flags = '';
0567 else
0568 flags = varargin{3};
0569 end
0570 if isempty(flags), flags = ' '; end
0571 o = varargin{2};
0572 varargout = {[]};
0573
0574
0575 if ~any(flags=='n')
0576 d = spm_input('Description of ROI', '+1', 's', descrip(o));
0577 o = descrip(o,d);
0578 l = spm_input('Label for ROI', '+1', 's', label(o));
0579 o = label(o,l);
0580 end
0581
0582 fn = source(o);
0583 if isempty(fn) || any(flags=='l')
0584 fn = maroi('filename', mars_utils('str2fname', label(o)));
0585 end
0586
0587 f_f = ['*' maroi('classdata', 'fileend')];
0588 [f p] = mars_uifile('put', ...
0589 {f_f, ['ROI files (' f_f ')']},...
0590 'File name for ROI', fn);
0591 if any(f~=0)
0592 roi_fname = maroi('filename', fullfile(p, f));
0593 try
0594 varargout = {saveroi(o, roi_fname)};
0595 catch
0596 warning([lasterr ' Error saving ROI to file ' roi_fname])
0597 end
0598 end
0599
0600
0601 case 'combinerois'
0602
0603
0604
0605 roilist = spm_get(Inf,['*' maroi('classdata', 'fileend')], ...
0606 'Select ROI(s) to combine');
0607 if isempty(roilist)
0608 return
0609 end
0610 roilist = maroi('load_cell', roilist);
0611 [Finter,Fgraph,CmdLine] = spm('FnUIsetup','Combine ROIs');
0612 spm_input('(r1 & r2) & ~r3',1,'d','Example function:');
0613 func = spm_input('Function to combine ROIs', '+1', 's', '');
0614 if isempty(func), retnrn, end
0615 for i = 1:length(roilist)
0616 eval(sprintf('r%d = roilist{%d};', i, i));
0617 end
0618 try
0619 eval(['o=' func ';']);
0620 catch
0621 warning(['Hmm, probem with function ' func ': ' lasterr]);
0622 return
0623 end
0624 if isempty(o)
0625 warning('Empty object resulted');
0626 return
0627 end
0628 if is_empty_roi(o)
0629 warning('No volume resulted for ROI');
0630 return
0631 end
0632
0633
0634 if isa(o, 'maroi')
0635 o = label(o, func);
0636 o = marsbar('saveroi', o);
0637 if ~isempty(o)
0638 fprintf('\nSaved ROI as %s\n', source(o));
0639 end
0640 else
0641 warning(sprintf('\nNo ROI resulted from function %s...\n', func));
0642 end
0643
0644
0645 case 'flip_lr'
0646
0647
0648
0649 roilist = spm_get([0 1],['*' maroi('classdata', 'fileend')],...
0650 'Select ROI to flip L/R');
0651 if isempty(roilist)
0652 return
0653 end
0654 [Finter,Fgraph,CmdLine] = spm('FnUIsetup','Flip ROI L<->R');
0655 o = maroi('load', roilist);
0656 o = flip_lr(o);
0657
0658
0659 o = marsbar('saveroi', o, 'l');
0660 fprintf('\nSaved ROI as %s\n', source(o));
0661
0662
0663 case 'show_volume'
0664
0665
0666
0667 roi_names = spm_get([0 Inf], '*roi.mat', 'Select ROIs tp get volume');
0668 if isempty(roi_names),return,end
0669 rois = maroi('load_cell', roi_names);
0670 for i = 1:size(rois, 1)
0671 fprintf('Volume of %s: %6.2f\n', source(rois{i}), volume(rois{i}));
0672 end
0673 return
0674
0675
0676 case 'roi_as_image'
0677
0678
0679
0680 [Finter,Fgraph,CmdLine] = spm('FnUIsetup','Write ROI to image');
0681
0682 roi = spm_get([0 1], '*roi.mat', 'Select ROI to write');
0683 if isempty(roi),return,end
0684 [pn fn ext] = fileparts(roi);
0685 roi = maroi('load', roi);
0686
0687
0688 spopts = {'spacebase','image'};
0689 splabs = {'Base space for ROIs','From image'};
0690 if has_space(roi)
0691 spopts = {spopts{:} 'native'};
0692 splabs = {splabs{:} 'ROI native space'};
0693 end
0694 spo = spm_input('Space for ROI image', '+1', 'm',splabs,...
0695 spopts, 1);
0696 switch char(spo)
0697 case 'spacebase'
0698 sp = maroi('classdata', 'spacebase');
0699 case 'image'
0700 img = spm_get([0 1], mars_veropts('get_img_ext'), 'Image defining space');
0701 if isempty(img),return,end
0702 sp = mars_space(img);
0703 case 'native'
0704 sp = [];
0705 end
0706
0707
0708 gend = maroi('classdata', 'fileend');
0709 lg = length(gend);
0710 f2 = [fn ext];
0711 if length(f2)>=lg && strcmp(gend, [f2(end - lg +1 : end)])
0712 f2 = f2(1:end-lg);
0713 else
0714 f2 = fn;
0715 end
0716
0717 fname = mars_utils('get_img_name', f2);
0718 if isempty(fname), return, end
0719 save_as_image(roi, fname, sp);
0720 fprintf('Saved ROI as %s\n',fname);
0721
0722
0723 case 'attach_image'
0724
0725
0726
0727 if nargin < 2
0728 V = spm_get([0 1], mars_veropts('get_img_ext'), 'Image to attach');
0729 if isempty(V), return, end
0730 else
0731 V = varargin{1};
0732 end
0733 if nargin < 3
0734 rois = spm_get([0 Inf], ['*' maroi('classdata', 'fileend')], ...
0735 'Select ROIs to attach image to');
0736
0737 if isempty(rois), return, end
0738 else
0739 rois = varargin{2};
0740 end
0741 if ischar(V), V = spm_vol(V); end
0742 for i = 1:size(rois, 1)
0743 n = deblank(rois(i,:));
0744 try
0745 r = maroi('load', n);
0746 catch
0747 r = []
0748 if ~strmatch(lasterr, 'Cant map image file.')
0749 error(lasterr);
0750 end
0751 end
0752 if isempty(r)
0753 continue
0754 end
0755 if ~isa(r, 'maroi_image')
0756 fprintf('ROI %s is not an image ROI - ignored\n', n);
0757 continue
0758 end
0759
0760 r = vol(r, V);
0761 saveroi(r, n);
0762 fprintf('Saved ROI %s, attached to image %s\n',...
0763 n, V.fname)
0764 end
0765 return
0766
0767
0768 case 'make_design'
0769
0770
0771
0772 if nargin < 2
0773 des_type = 'basic';
0774 else
0775 des_type = varargin{2};
0776 end
0777 if sf_prev_save('def_design') == -1, return, end
0778 D = ui_build(mars_veropts('default_design'), des_type);
0779 mars_arm('set', 'def_design', D);
0780 marsbar('design_report');
0781
0782
0783 case 'list_images'
0784
0785
0786
0787 marsD = mars_arm('get', 'def_design');
0788 if isempty(marsD), return, end;
0789 if has_images(marsD)
0790 P = image_names(marsD);
0791 strvcat(P{:})
0792 else
0793 disp('Design does not contain images');
0794 end
0795
0796
0797 case 'check_images'
0798
0799
0800
0801 marsD = mars_arm('get', 'def_design');
0802 if isempty(marsD), return, end;
0803 if ~has_images(marsD)
0804 disp('Design does not contain images');
0805 return
0806 end
0807
0808 P = image_names(marsD);
0809 P = strvcat(P{:});
0810 ok_f = 1;
0811 for i = 1:size(P, 1)
0812 fname = deblank(P(i,:));
0813 if ~exist(fname, 'file');
0814 fprintf('Image %d: %s does not exist\n', i, fname);
0815 ok_f = 0;
0816 end
0817 end
0818 if ok_f
0819 disp('All images in design appear to exist');
0820 end
0821
0822
0823 case 'ana_cd'
0824
0825
0826
0827 marsD = mars_arm('get', 'def_design');
0828 if isempty(marsD), return, end;
0829
0830
0831 [Finter,Fgraph,CmdLine] = spm('FnUIsetup','Change image path in design', 0);
0832
0833
0834 P = image_names(marsD);
0835 P = strvcat(P{:});
0836 root_names = spm_str_manip(P, 'H');
0837 spm_input(deblank(root_names(1,:)),1,'d','Common path is:');
0838
0839
0840 newpath = spm_get([-1 0], '', 'New directory root for files');
0841 if isempty(newpath), return, end
0842
0843
0844 marsD = cd_images(marsD, newpath);
0845 mars_arm('set', 'def_design', marsD);
0846
0847
0848 case 'ana_desmooth'
0849
0850
0851
0852 marsD = mars_arm('get', 'def_design');
0853 if isempty(marsD), return, end;
0854 marsD = prefix_images(marsD, 'remove', 's');
0855 mars_arm('set', 'def_design', marsD);
0856 disp('Done');
0857
0858
0859 case 'add_images'
0860
0861
0862
0863 marsD = mars_arm('get', 'def_design');
0864 if isempty(marsD), return, end
0865 if ~is_fmri(marsD), return, end
0866 marsD = fill(marsD, {'images'});
0867 mars_arm('update', 'def_design', marsD);
0868 mars_arm('set_param', 'def_design', 'file_name', '');
0869 mars_arm('show_summary', 'def_design');
0870
0871
0872 case 'edit_filter'
0873
0874
0875
0876 marsD = mars_arm('get', 'def_design');
0877 if isempty(marsD), return, end
0878 if ~is_fmri(marsD), return, end
0879 tmp = {'filter'};
0880 if ~strcmp(type(marsD), 'SPM99'), tmp = [tmp {'autocorr'}]; end
0881 marsD = fill(marsD, tmp);
0882 mars_arm('update', 'def_design', marsD);
0883 mars_arm('set_param', 'def_design', 'file_name', '');
0884 mars_arm('show_summary', 'def_design');
0885
0886
0887 case 'def_from_est'
0888
0889
0890
0891 marsE = mars_arm('get', 'est_design');
0892 if isempty(marsE), return, end;
0893 errf = mars_arm('set', 'def_design', marsE);
0894 if ~errf, marsbar('design_report'); end
0895
0896
0897 case 'set_def'
0898
0899
0900
0901 if mars_arm('set_ui', 'def_design'), return, end
0902 marsbar('design_report');
0903
0904
0905 case 'design_report'
0906
0907
0908
0909 marsD = mars_arm('get', 'def_design');
0910 if isempty(marsD), return, end;
0911 spm('FnUIsetup','Explore design', 0);
0912
0913 fprintf('%-40s: ','Design reporting');
0914 ui_report(marsD, 'DesMtx');
0915 ui_report(marsD, 'DesRepUI');
0916 fprintf('%30s\n','...done');
0917
0918
0919 case 'design_filter'
0920
0921
0922
0923 marsD = mars_arm('get', 'def_design');
0924 if isempty(marsD), return, end;
0925 marsY = mars_arm('get', 'roi_data');
0926 if isempty(marsY), return, end
0927
0928 if mars_arm('isempty', 'def_design')
0929 error('Need data and design with matching number of rows');
0930 end
0931 ui_ft_design_data(marsD, marsY);
0932
0933
0934 case 'extract_data'
0935
0936
0937
0938 if nargin < 2
0939 etype = 'default';
0940 else
0941 etype = varargin{2};
0942 end
0943 if nargin < 3
0944 roi_list = '';
0945 else
0946 roi_list = varargin{3};
0947 end
0948
0949 varargout = {[]};
0950
0951
0952 if sf_prev_save('roi_data') == -1, return, end
0953 if isempty(roi_list)
0954 roi_list = spm_get(Inf,'*roi.mat','Select ROI(s) to extract data for');
0955 end
0956 if isempty(roi_list), return, end
0957
0958 [Finter,Fgraph,CmdLine] = spm('FnUIsetup','Extract data', 0);
0959
0960 if strcmp(etype, 'default')
0961 marsD = mars_arm('get', 'def_design');
0962 if isempty(marsD), return, end;
0963 if ~has_images(marsD),
0964 marsD = fill(marsD, 'images');
0965 mars_arm('update', 'def_design', marsD);
0966 end
0967 VY = marsD;
0968 row = block_rows(marsD);
0969 else
0970
0971
0972 marsD = [];
0973 if spm_input('Use SPM design?', '+1', 'b', 'Yes|No', [1 0], 1)
0974 marsD = mars_arm('get', 'def_design');
0975 if ~has_images(marsD),
0976 marsD = fill(marsD, 'images');
0977 mars_arm('update', 'def_design', marsD);
0978 end
0979 end
0980 [VY row] = mars_image_scaling(marsD);
0981 end
0982
0983
0984 sumfunc = sf_get_sumfunc(MARS.OPTIONS.statistics.sumfunc);
0985
0986
0987 o = maroi('load_cell', roi_list);
0988
0989
0990 marsY = get_marsy(o{:}, VY, sumfunc, 'v');
0991 marsY = block_rows(marsY, row);
0992 if ~n_regions(marsY)
0993 msgbox('No data returned','Data extraction', 'warn');
0994 return
0995 end
0996
0997
0998 mars_arm('set', 'roi_data', marsY);
0999 mars_arm('show_summary', 'roi_data');
1000
1001 varargout = {marsY};
1002
1003
1004 case 'plot_data'
1005
1006
1007
1008
1009
1010
1011 if nargin < 2
1012 p_type = [];
1013 else
1014 p_type = varargin{2};
1015 end
1016 if isempty(p_type)
1017 p_type = 'full';
1018 end
1019 marsY = mars_arm('get', 'roi_data');
1020 if isempty(marsY), return, end
1021
1022 [Finter,Fgraph,CmdLine] = spm('FnUIsetup','Plot data', 0);
1023 if strcmp(p_type, 'full')
1024 if ~mars_arm('isempty', 'def_design')
1025 D = mars_arm('get', 'def_design');
1026 if isempty(D), return, end
1027 if has_filter(D)
1028 if spm_input('Use design filter?', '+1', 'y/n', [1 0], 1)
1029 flags = {};
1030 if has_whitener(D)
1031 if ~spm_input('Use whitening filter?', '+1', 'y/n', [1 0], 1)
1032 flags = 'no_whitening';
1033 end
1034 end
1035 marsY = apply_filter(D, marsY, flags);
1036 end
1037 end
1038 end
1039 p_type = char(spm_input('Type of plot', '+1', 'm', ...
1040 'All|Time course|FFT|ACF', ...
1041 {'all','raw','fft','acf'}));
1042 end
1043
1044 ns = region_name(marsY);
1045 rno = mars_struct('getifthere', MARS, 'WORKSPACE', 'default_region');
1046 if ~isempty(rno)
1047 fprintf('Using default region: %s\n', ns{rno});
1048 end
1049 ui_plot(marsY, struct('types', p_type, 'r_nos', rno));
1050
1051
1052 case 'import_data'
1053
1054
1055
1056
1057
1058 if sf_prev_save('roi_data') == -1, return, end
1059
1060 [Finter,Fgraph,CmdLine] = spm('FnUIsetup','Import data', 0);
1061
1062 r_f = spm_input('Import what?', '+1', 'm', ...
1063 ['Sample time courses for one region'...
1064 '|Summary time course(s) for region(s)'],...
1065 [1 0], 2);
1066
1067 Ls = ['Matlab workspace' ...
1068 '|Text file',...
1069 '|Lotus spreadsheet'];,...
1070 Os = {'matlab','txt','wk1'};
1071
1072 if ~isempty(which('xlsread'))
1073 Ls = [Ls '|Excel spreadsheet'];
1074 Os = [Os {'xls'}];
1075 end
1076
1077 src = spm_input('Import fron?', '+1', 'm', Ls, Os, 1);
1078
1079 switch src{1}
1080 case 'matlab'
1081 Y = spm_input('Matlab expression', '+1', 'e');
1082 fn = 'Matlab input';
1083 pn_fn = lower(fn);
1084 case 'txt'
1085 [fn, pn] = mars_uifile('get', ...
1086 {'*.txt;*.dat;*.csv', 'Text files (*.txt, *.dat, *.csv)'; ...
1087 '*.*', 'All Files (*.*)'}, ...
1088 'Select a text file');
1089 if isequal(fn,0), return, end
1090 pn_fn = fullfile(pn, fn);
1091 Y = spm_load(pn_fn);
1092 case 'wk1'
1093 [fn, pn] = mars_uifile('get', ...
1094 {'*.wk1', 'Lotus spreadsheet files (*.wk1)'; ...
1095 '*.*', 'All Files (*.*)'}, ...
1096 'Select a Lotus file');
1097 if isequal(fn,0), return, end
1098 pn_fn = fullfile(pn, fn);
1099 Y = wk1read(pn_fn);
1100 case 'xls'
1101 [fn, pn] = mars_uifile('get', ...
1102 {'*.xls', 'Excel spreadsheet files (*.xls)'; ...
1103 '*.*', 'All Files (*.*)'}, ...
1104 'Select an Excel file');
1105 if isequal(fn,0), return, end
1106 pn_fn = fullfile(pn, fn);
1107 Y = xlsread(pn_fn);
1108 otherwise
1109 error('Strange source');
1110 end
1111 if r_f
1112 s_f = sf_get_sumfunc(MARS.OPTIONS.statistics.sumfunc);
1113 r_st = struct('name', fn,...
1114 'descrip', pn_fn);
1115 s_st = struct('descrip', ['Region data loaded from ' pn_fn],...
1116 'sumfunc', s_f);
1117 marsY = marsy({Y},r_st, s_st);
1118 pref = '';
1119 else
1120 s_st = struct('descrip', ['Summary data loaded from ' pn_fn]);
1121 marsY = marsy(Y, '', s_st);
1122 pref = spm_input('Prefix for region names', '+1', 's', [fn '_']);
1123 end
1124
1125
1126 stop_f = 0;
1127 ns = region_name(marsY, [], [], pref);
1128 spm_input('Return name with spaces only to abort entry','+1','d');
1129 for r = 1:length(ns)
1130 ns{r} = spm_input(...
1131 sprintf('Name for region %d', r),...
1132 '+1', 's', ns{r});
1133 if all(ns{r}==' '), stop_f = 1; break, end
1134 end
1135 if ~stop_f
1136 marsY = region_name(marsY, [], ns);
1137 end
1138
1139 mars_arm('set', 'roi_data', marsY);
1140 mars_arm('show_summary', 'roi_data');
1141 disp(['Data loaded from ' pn_fn]);
1142
1143
1144 case 'export_data'
1145
1146
1147
1148 marsY = mars_arm('get', 'roi_data');
1149 if isempty(marsY), return, end
1150
1151 [Finter,Fgraph,CmdLine] = spm('FnUIsetup','Export data', 0);
1152
1153 r_f = spm_input('Export what?', '+1', 'm', ...
1154 ['Sample time courses for one region'...
1155 '|Summary time course(s) for region(s)'],...
1156 [1 0], 2);
1157
1158 Ls = ['Matlab workspace' ...
1159 '|Text file',...
1160 '|Lotus spreadsheet'];,...
1161 Os = {'matlab','txt','wk1'};
1162
1163 if ~isempty(which('xlswrite'))
1164 xls_write = 1;
1165 elseif ~isempty(which('xlswrite5'))
1166 xls_write = 2;
1167 else
1168 xls_write = 0;
1169 end
1170
1171 if xls_write
1172 Ls = [Ls '|Excel spreadsheet'];
1173 Os = [Os {'xls'}];
1174 end
1175
1176 src = spm_input('Export to?', '+1', 'm', Ls, Os, 1);
1177
1178 if r_f
1179 rno = marsbar('get_region', region_name(marsY));
1180 Y = region_data(marsY, rno);
1181 Y = Y{1};
1182 else
1183 Y = summary_data(marsY);
1184 end
1185
1186 switch src{1}
1187 case 'matlab'
1188 str = '';
1189 while ~mars_utils('is_valid_varname', str)
1190 str = spm_input('Matlab variable name', '+1', 's');
1191 if isempty(str), return, end
1192 end
1193 assignin('base', str, Y);
1194 fn = ['Matlab variable: ' str];
1195 case 'txt'
1196 [fn, pn] = mars_uifile('put', ...
1197 {'*.txt;*.dat;*.csv', 'Text files (*.txt, *.dat, *.csv)'; ...
1198 '*.*', 'All Files (*.*)'}, ...
1199 'Text file name');
1200 if isequal(fn,0), return, end
1201 save(fullfile(pn,fn), 'Y', '-ascii');
1202 case 'wk1'
1203 [fn, pn] = mars_uifile('put', ...
1204 {'*.wk1', 'Lotus spreadsheet files (*.wk1)'; ...
1205 '*.*', 'All Files (*.*)'}, ...
1206 'Lotus spreadsheet file');
1207 if isequal(fn,0), return, end
1208 wk1write(fullfile(pn,fn), Y);
1209 case 'xls'
1210 [fn, pn] = mars_uifile('put', ...
1211 {'*.xls', 'Excel spreadsheet files (*.xls)'; ...
1212 '*.*', 'All Files (*.*)'}, ...
1213 'Excel spreadsheet file');
1214 if isequal(fn,0), return, end
1215 if xls_write == 1
1216 xlswrite(fullfile(pn,fn), Y);
1217 else
1218 xlswrite5(fullfile(pn,fn), Y);
1219 end
1220 otherwise
1221 error('Strange source');
1222 end
1223 disp(['Data saved to ' fn]);
1224
1225
1226 case 'split_data'
1227
1228
1229
1230 marsY = mars_arm('get', 'roi_data');
1231 if isempty(marsY), return, end
1232 if n_regions(marsY) == 1
1233 disp('Only one region in ROI data');
1234 return
1235 end
1236
1237
1238 [Finter,Fgraph,CmdLine] = spm('FnUIsetup','Split regions to files', 0);
1239
1240 d = spm_get([-1 0], '', 'New directory root for files');
1241 if isempty(d), return, end
1242
1243 def_f = summary_descrip(marsY);
1244 if ~isempty(def_f)
1245 def_f = mars_utils('str2fname', def_f);
1246 end
1247 f = spm_input('Root filename for regions', '+1', 's', def_f);
1248 f = mars_utils('str2fname', f);
1249 mYarr = split(marsY);
1250 for i = 1:length(mYarr)
1251 fname = fullfile(d, sprintf('%s_region_%d_mdata.mat', f, i));
1252 savestruct(mYarr(i), fname);
1253 fprintf('Saved region %d as %s\n', i, fname);
1254 end
1255
1256
1257 case 'join_data'
1258
1259
1260
1261
1262
1263 if sf_prev_save('roi_data') == -1, return, end
1264
1265 P = spm_get([0 Inf], '*_mdata.mat', 'Select data files to join');
1266
1267 if isempty(P), return, end
1268 for i = 1:size(P,1)
1269 d_o{i} = marsy(deblank(P(i,:)));
1270 end
1271 marsY = join(d_o{:});
1272 mars_arm('set', 'roi_data', marsY);
1273 mars_arm('show_summary', 'roi_data');
1274 disp(P)
1275 disp('Files merged and set as current data')
1276
1277
1278 case 'estimate'
1279
1280
1281
1282
1283
1284
1285 marsD= mars_arm('get', 'def_design');
1286 if isempty(marsD), return, end
1287 marsY = mars_arm('get', 'roi_data');
1288 if isempty(marsY), return, end
1289 if mars_arm('isempty', 'def_design')
1290 error('Need design and data with matching number of rows');
1291 end
1292 if sf_prev_save('est_design') == -1, return, end
1293 if ~can_mars_estimate(marsD)
1294 marsD = fill(marsD, 'for_estimation');
1295 mars_arm('update', 'def_design', marsD);
1296 end
1297 marsRes = estimate(marsD, marsY, struct(...
1298 'redo_covar', 1, 'redo_whitening', 1));
1299 mars_arm('set', 'est_design', marsRes);
1300 mars_arm('show_summary', 'est_design');
1301
1302
1303 case 'set_results'
1304
1305
1306
1307
1308
1309 varargout = {0};
1310
1311
1312 if sf_prev_save('est_design') == -1, return, end
1313 if sf_prev_save('roi_data') == -1, return, end
1314
1315
1316 mars_arm('set_ui', 'est_design');
1317 if mars_arm('isempty', 'est_design'), return, end
1318
1319
1320 marsRes = mars_arm('get', 'est_design');
1321 mars_arm('set', 'roi_data', get_data(marsRes));
1322
1323
1324 if mars_struct('isthere', MARS, 'WORKSPACE', 'default_contrast')
1325 MARS.WORKSPACE.default_contrast = [];
1326 fprintf('Reset of estimated design, cleared default contrast...\n');
1327 end
1328
1329
1330 fprintf('%-40s: ','Design reporting');
1331 ui_report(marsRes, 'DesMtx');
1332 ui_report(marsRes, 'DesRepUI');
1333 fprintf('%30s\n','...done');
1334
1335 varargout = {1};
1336 return
1337
1338
1339 case 'plot_residuals'
1340
1341
1342
1343 marsRes = mars_arm('get', 'est_design');
1344 if isempty(marsRes), return, end
1345 Y = residuals(marsRes);
1346 ns = region_name(Y);
1347 rno = mars_struct('getifthere', MARS, 'WORKSPACE', 'default_region');
1348 if ~isempty(rno)
1349 fprintf('Using default region: %s\n', ns{rno});
1350 end
1351 [Finter,Fgraph,CmdLine] = spm('FnUIsetup','Plot residuals', 1);
1352 p_type = char(spm_input('Type of plot', '+1', 'm', ...
1353 'All|Time course|FFT|ACF', ...
1354 {'all','raw','fft','acf'}));
1355 ui_plot(Y, struct('types', p_type, 'r_nos', rno));
1356
1357
1358 case 'set_defcon'
1359
1360
1361
1362 varargout = {[]};
1363 marsRes = mars_arm('get', 'est_design');
1364 if isempty(marsRes), return, end
1365
1366
1367 [Finter,Fgraph,CmdLine] = spm('FnUIsetup','Default contrast', 0);
1368 Ic = mars_struct('getifthere',MARS, 'WORKSPACE', 'default_contrast');
1369 if isempty(Ic)
1370 cname = '[Not set]';
1371 else
1372 xCon = get_contrasts(marsRes);
1373 cname = xCon(Ic).name;
1374 end
1375 spm_input(cname, 1, 'd', 'Default contrast');
1376 opts = {'Quit', 'Set new default'};
1377 if ~isempty(Ic), opts = [opts {'Clear default contrast'}]; end
1378 switch spm_input('What to do?', '+1', 'm', opts, [1:length(opts)], 1);
1379 case 1
1380 case 2
1381 [Ic marsRes changef] = ui_get_contrasts(marsRes, 'T|F',1,...
1382 'Select default contrast','',1);
1383 if changef
1384 mars_arm('update', 'est_design', marsRes);
1385 end
1386 case 3
1387 Ic = [];
1388 end
1389 MARS.WORKSPACE.default_contrast = Ic;
1390 varargout = {Ic};
1391
1392
1393 case 'set_defregion'
1394
1395
1396
1397 varargout = {[]};
1398 marsY = mars_arm('get', 'roi_data');
1399 if isempty(marsY), return, end
1400 ns = region_name(marsY);
1401 if length(ns) == 1
1402 disp('Only one region in data');
1403 MARS.WORKSPACE.default_region = 1;
1404 varargout = {1};
1405 return
1406 end
1407
1408
1409 [Finter,Fgraph,CmdLine] = spm('FnUIsetup','Default region', 0);
1410 rno = mars_struct('getifthere',MARS, 'WORKSPACE', 'default_region');
1411 if isempty(rno), rname = '[Not set]'; else rname = ns{rno}; end
1412 spm_input(rname, 1, 'd', 'Default region:');
1413 opts = {'Quit', 'Set new default'};
1414 if ~isempty(rno), opts = [opts {'Clear default region'}]; end
1415 switch spm_input('What to do?', '+1', 'm', opts, [1:length(opts)], 1);
1416 case 1
1417 case 2
1418 rno = marsbar('get_region', ns);
1419 disp(['Default region set to: ' ns{rno}]);
1420 case 3
1421 rno = [];
1422 end
1423 MARS.WORKSPACE.default_region = rno;
1424 varargout = {rno};
1425
1426
1427 case 'get_region'
1428
1429
1430
1431
1432
1433
1434
1435 if nargin < 2
1436 error('Need region names to select from');
1437 else
1438 names = varargin{2};
1439 end
1440 if nargin < 3
1441 prompt = 'Select region';
1442 else
1443 prompt = varargin{3};
1444 end
1445
1446
1447 maxlist = 200;
1448 if length(names) > maxlist
1449
1450 error('Too many regions');
1451 end
1452 if length(names) == 1
1453 rno = 1;
1454 elseif isempty(names)
1455 rno = []
1456 else
1457
1458 rno = spm_input(prompt, '+1', 'm', names);
1459 end
1460 varargout = {rno};
1461
1462
1463 case 'spm_graph'
1464
1465
1466
1467 marsRes = mars_arm('get', 'est_design');
1468 if isempty(marsRes), return, end
1469
1470
1471 [Finter,Fgraph,CmdLine] = spm('FnUIsetup','Mars SPM graph', 1);
1472
1473 ns = region_name(get_data(marsRes));
1474 rno = mars_struct('getifthere', MARS, 'WORKSPACE', 'default_region');
1475 if ~isempty(rno)
1476 fprintf('Using default region: %s\n', ns{rno});
1477 else
1478 rno = marsbar('get_region', ns, 'Select region to plot');
1479 end
1480
1481 Ic = mars_struct('getifthere', MARS, 'WORKSPACE', 'default_contrast');
1482 if ~isempty(Ic)
1483 xCon = get_contrasts(marsRes);
1484 fprintf('Using default contrast: %s\n', xCon(Ic).name);
1485 end
1486
1487
1488
1489 [r_st marsRes changef] = mars_spm_graph(marsRes, rno, Ic);
1490
1491
1492 fns = fieldnames(r_st);
1493 for f = 1:length(fns)
1494 assignin('base', fns{f}, getfield(r_st, fns{f}));
1495 end
1496
1497
1498 if changef
1499 mars_arm('update', 'est_design', marsRes);
1500 end
1501
1502
1503 case 'stat_table'
1504
1505
1506
1507 marsRes = mars_arm('get', 'est_design');
1508 if isempty(marsRes), return, end
1509 Ic = mars_struct('getifthere', MARS, 'WORKSPACE', 'default_contrast');
1510 if ~isempty(Ic)
1511 xCon = get_contrasts(marsRes);
1512 fprintf('Using default contrast: %s\n', xCon(Ic).name);
1513 end
1514 [strs marsS marsRes changef] = ...
1515 stat_table(marsRes, Ic);
1516 disp(char(strs));
1517 assignin('base', 'marsS', marsS);
1518 if changef
1519 mars_arm('update', 'est_design', marsRes);
1520 end
1521
1522
1523 case 'signal_change'
1524
1525
1526
1527 marsRes = mars_arm('get', 'est_design');
1528 if isempty(marsRes), return, end
1529 if ~is_fmri(marsRes)
1530 fprintf('Need FMRI design for %% signal change\n');
1531 return
1532 end
1533
1534
1535 [Finter,Fgraph,CmdLine] = spm('FnUIsetup','Percent signal change', 0);
1536
1537 [marsRes ic status] = ui_event_types(marsRes);
1538 if (status==0), return, end
1539 if (status>1), mars_arm('update', 'est_design', marsRes); end
1540 if isempty(ic), return, end
1541
1542 dur = spm_input('Event duration', '+1', 'e', 0);
1543
1544
1545 diff_func = mars_struct('getifthere', MARS, 'OPTIONS', ...
1546 'events', 'diff_func');
1547 if isempty(diff_func), diff_func = 'max abs';
1548 elseif strcmp(diff_func, 'window')
1549 spm_input('Event signal change window...', '+1','d', mfilename);
1550 times = spm_input('Mean signal between times', ...
1551 '+1', 'r', [4 6], 2, [0 dur+32]);
1552 other_args = {times, bf_dt(marsRes)};
1553 else
1554 other_args = {};
1555 end
1556
1557 ic_len = length(ic);
1558 et = event_types(marsRes);
1559 for i = 1:ic_len
1560 pc(i,:) = event_signal(marsRes, et(ic(i)).e_spec, dur, ...
1561 diff_func, ...
1562 other_args{:});
1563 end
1564 rns = region_name(get_data(marsRes));
1565 disp('Sort-of % signal change');
1566 disp(sprintf('Duration: %3.2f seconds', dur));
1567 for i = 1:ic_len
1568 disp(['Event: ' et(ic(i)).name]);
1569 for r = 1:length(rns)
1570 disp(sprintf('Region: %40s; %5.3f', rns{r}, pc(i, r)));
1571 end
1572 end
1573 assignin('base', 'pc', pc);
1574
1575
1576 case 'fitted_events'
1577
1578
1579
1580 marsRes = mars_arm('get', 'est_design');
1581 if isempty(marsRes), return, end
1582 if ~is_fmri(marsRes)
1583 fprintf('Need FMRI design for fitted event time courses\n');
1584 return
1585 end
1586
1587
1588 [Finter,Fgraph,CmdLine] = spm('FnUIsetup','Fitted events', 1);
1589
1590 [marsRes ic status] = ui_event_types(marsRes);
1591 if (status==0), return, end
1592 if (status>1), mars_arm('update', 'est_design', marsRes); end
1593 if isempty(ic), return, end
1594
1595 dur = spm_input('Event duration', '+1', 'e', 0);
1596 ic_len = length(ic);
1597 et = event_types(marsRes);
1598 for i = 1:ic_len
1599 [tc{i} dt] = event_fitted(marsRes, et(ic(i)).e_spec, dur);
1600 end
1601
1602 if ic_len > 8
1603 warning('Too many event types to plot, plotting first 8');
1604 ic_len = 8;
1605 end
1606
1607 figure(Fgraph);
1608 if ic_len > 1, p_cols = 2; else p_cols = 1; end
1609 p_rows = ceil(ic_len / p_cols);
1610 last_row_starts = (p_rows-1) * p_cols + 1;
1611 for i = 1:ic_len
1612 t = tc{i};
1613 secs = ([1:size(t, 1)]-1) * dt;
1614 subplot(p_rows, p_cols, i);
1615 plot(secs, t);
1616 title(et(ic(i)).name);
1617 if i >= last_row_starts, xlabel('Seconds'); end
1618 if rem(i-1, p_cols)==0, ylabel('Signal change'); end
1619 end
1620
1621 legend(region_name(get_data(marsRes)));
1622
1623 assignin('base', 'time_courses', tc);
1624 assignin('base', 'dt', dt);
1625
1626
1627 case 'fir_events'
1628
1629
1630
1631 marsRes = mars_arm('get', 'est_design');
1632 if isempty(marsRes), return, end
1633 if ~is_fmri(marsRes)
1634 fprintf('Need FMRI design for FIR event time courses\n');
1635 return
1636 end
1637
1638
1639 [Finter,Fgraph,CmdLine] = spm('FnUIsetup','FIR for events', 1);
1640
1641 [marsRes ic status] = ui_event_types(marsRes);
1642 if (status==0), return, end
1643 if (status>1), mars_arm('update', 'est_design', marsRes); end
1644 if isempty(ic), return, end
1645
1646 et = event_types(marsRes);
1647 ic_len = length(ic);
1648
1649
1650
1651
1652
1653 d_a = []; opts = [];
1654 for i = 1:ic_len
1655 e_spec = et(ic(i)).e_spec;
1656 for j = 1:size(e_spec, 2)
1657 [o d] = event_onsets(marsRes, e_spec(:, j));
1658 d_a = [d_a; d];
1659 end
1660 end
1661 if any(d_a) && ~any(diff(d_a))
1662 if spm_input('FIR type', '+1','m',...
1663 'Single|Stacked', [1 0], 1)
1664 opts.single = 1;
1665 end
1666 end
1667 if spm_input('Signal units', '+1','m',...
1668 'Percent|Beta units', [1 0], 1)
1669 opts.percent = 1;
1670 end
1671
1672 bin_length = spm_input('Bin length (secs)', '+1', 'e', tr(marsRes));
1673 def_bin_no = round(25/bin_length);
1674 bin_no = spm_input('No of bins', '+1', 'e', def_bin_no);
1675
1676 for i = 1:ic_len
1677 tc{i} = event_fitted_fir(marsRes, ...
1678 et(ic(i)).e_spec, ...
1679 bin_length, ...
1680 bin_no, ...
1681 opts);
1682 end
1683
1684 if ic_len > 8
1685 warning('Too many event types to plot, plotting first 8');
1686 ic_len = 8;
1687 end
1688
1689 figure(Fgraph);
1690 if ic_len > 1, p_cols = 2; else p_cols = 1; end
1691 p_rows = ceil(ic_len / p_cols);
1692 last_row_starts = (p_rows-1) * p_cols + 1;
1693 secs = ([1:bin_no]-1) * bin_length + bin_length/2;
1694 for i = 1:ic_len
1695 t = tc{i};
1696 subplot(p_rows, p_cols, i);
1697 plot(secs, t);
1698 title(et(ic(i)).name);
1699 if i >= last_row_starts, xlabel('Seconds'); end
1700 if rem(i-1, p_cols)==0, ylabel('Signal change'); end
1701 end
1702 legend(region_name(get_data(marsRes)));
1703
1704 assignin('base', 'time_courses', tc);
1705 assignin('base', 'bin_length', bin_length);
1706 assignin('base', 'bin_no', bin_no);
1707
1708
1709 case 'add_events_by_name'
1710
1711
1712
1713 D = mars_arm('get', 'est_design');
1714 if isempty(D), return, end
1715 if ~is_fmri(D)
1716 disp('Can only add event types to FMRI designs');
1717 return
1718 end
1719 et = event_types(D);
1720 et = [et event_types_named(D)];
1721 D = event_types(D, et);
1722 mars_arm('update', 'est_design', D);
1723
1724
1725 case 'merge_contrasts'
1726
1727
1728
1729 D = mars_arm('get', 'est_design');
1730 if isempty(D), return, end
1731 filter_spec = {...
1732 'SPM.mat','SPM: SPM.mat';...
1733 '*_mres.mat','MarsBaR: *_mres.mat';...
1734 '*x?on.mat','xCon.mat file'};
1735 [fn pn] = mars_uifile('get', ...
1736 filter_spec, ...
1737 'Source design/contrast file...');
1738 if isequal(fn,0) || isequal(pn,0), return, end
1739 fname = fullfile(pn, fn);
1740 D2 = mardo(fname);
1741
1742
1743 if ~has_contrasts(D2)
1744 error(['Cannot find contrasts in design/contrast file ' fname]);
1745 end
1746
1747
1748 if ~is_valid(D2)
1749 D2 = get_contrasts(D2);
1750 end
1751
1752 [D Ic changef] = add_contrasts(D, D2, 'ui');
1753 disp('Done');
1754 if changef
1755 mars_arm('update', 'est_design', D);
1756 end
1757
1758
1759 case 'refresh_contrasts'
1760
1761
1762
1763 D = mars_arm('get', 'est_design');
1764 if isempty(D), return, end
1765 D = refresh_contrasts(D);
1766 disp('Refreshed contrasts');
1767 mars_arm('update', 'est_design', D);
1768
1769
1770 case 'add_trial_f'
1771
1772
1773
1774 D = mars_arm('get', 'est_design');
1775 if isempty(D), return, end
1776 if ~is_fmri(D)
1777 disp('Can only add trial specific F contrasts for FMRI designs');
1778 return
1779 end
1780 [D changef] = add_trial_f(D);
1781 disp('Done');
1782 if changef
1783 mars_arm('update', 'est_design', D);
1784 end
1785
1786
1787 case 'error_log'
1788
1789
1790
1791 if nargin < 2
1792 fname = 'error_log.mat';
1793 else
1794 fname = varargin{2};
1795 end
1796
1797 e_log = struct('last_error', lasterr, ...
1798 'm_ver', marsbar('ver'),...
1799 'mars', MARS);
1800 savestruct(fname, e_log);
1801 if ~isempty(which('zip'))
1802 zip([fname '.zip'], fname);
1803 fname = [fname '.zip'];
1804 end
1805 disp(['Saved error log as ' fname]);
1806
1807
1808 case 'mars_menu'
1809
1810
1811
1812
1813 [tstr pstr optfields optlabs] = deal(varargin{2:5});
1814 if nargin < 6
1815 optargs = cell(1, length(optfields));
1816 else
1817 optargs = varargin{6};
1818 end
1819
1820 [Finter,Fgraph,CmdLine] = spm('FnUIsetup',tstr);
1821 of_end = length(optfields)+1;
1822 my_task = spm_input(pstr, '+1', 'm',...
1823 {optlabs{:} 'Quit'},...
1824 [1:of_end],of_end);
1825 if my_task == of_end, return, end
1826 marsbar(optfields{my_task}{:});
1827
1828
1829 otherwise
1830
1831 error('Unknown action string')
1832
1833
1834 end
1835 return
1836
1837
1838 function sum_func = sf_get_sumfunc(sum_func)
1839 if strcmp(sum_func, 'ask')
1840 sum_func = char(spm_input('Summary function', '+1','m',...
1841 'Mean|Weighted mean|Median|1st eigenvector',...
1842 {'mean','wtmean','median','eigen1'}, 1));
1843 end
1844
1845 function btn = sf_prev_save(obj_name)
1846 btn = mars_arm('save_ui', obj_name, ...
1847 struct('ync', 1, ...
1848 'no_no_save', 1, ...
1849 'prompt_prefix', 'previous '));
1850
1851 if btn == 0
1852 mars_arm('set_param', obj_name, 'has_changed', 0);
1853 end
1854 return
1855
